/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
* Jalview - A Sequence Alignment Editor and Viewer
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.api.AlignCalcManagerI;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.api.OOMHandlerI;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
-import jalview.workers.AlignCalcManager;
-import jalview.workers.ConsensusThread;
-import jalview.workers.ConservationThread;
-import jalview.workers.StrucConsensusThread;
-import jalview.ws.jws2.dm.AAConsSettings;
import jalview.ws.params.AutoCalcSetting;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision: 1.141 $
*/
-public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI
+public class AlignViewport extends AlignmentViewport implements
+ SelectionSource, CommandListener
{
- int startRes;
-
- int endRes;
-
- int startSeq;
-
- int endSeq;
-
- boolean showJVSuffix = true;
-
- boolean showText = true;
-
- boolean showColourText = false;
-
- boolean showBoxes = true;
-
- boolean wrapAlignment = false;
-
- boolean renderGaps = true;
-
- boolean showSequenceFeatures = false;
-
- boolean showAnnotation = true;
-
- int charHeight;
-
- int charWidth;
-
- boolean validCharWidth;
-
- int wrappedWidth;
-
Font font;
- boolean seqNameItalics;
-
-
NJTree currentTree = null;
- boolean scaleAboveWrapped = false;
-
- boolean scaleLeftWrapped = true;
-
- boolean scaleRightWrapped = true;
-
- boolean showHiddenMarkers = true;
-
boolean cursorMode = false;
- /**
- * Keys are the feature types which are currently visible. Note: Values are
- * not used!
- */
- Hashtable featuresDisplayed = null;
-
boolean antiAlias = false;
- Rectangle explodedPosition;
+ private Rectangle explodedGeometry;
String viewName;
- boolean gatherViewsHere = false;
-
- Stack historyList = new Stack();
-
- Stack redoList = new Stack();
-
- Hashtable sequenceColours;
-
- int thresholdTextColour = 0;
-
- Color textColour = Color.black;
-
- Color textColour2 = Color.white;
+ /*
+ * Flag set true on the view that should 'gather' multiple views of the same
+ * sequence set id when a project is reloaded. Set false on all views when
+ * they are 'exploded' into separate windows. Set true on the current view
+ * when 'Gather' is performed, and also on the first tab when the first new
+ * view is created.
+ */
+ private boolean gatherViewsHere = false;
- boolean rightAlignIds = false;
+ private AnnotationColumnChooser annotationColumnSelectionState;
/**
* Creates a new AlignViewport object.
setAlignment(al);
if (hiddenColumns != null)
{
- this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null
- && hiddenColumns.getHiddenColumns().size() > 0)
- {
- hasHiddenColumns = true;
- }
- else
- {
- hasHiddenColumns = false;
- }
+ colSel = hiddenColumns;
}
init();
}
setAlignment(al);
if (hiddenColumns != null)
{
- this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null
- && hiddenColumns.getHiddenColumns().size() > 0)
- {
- hasHiddenColumns = true;
- }
- else
- {
- hasHiddenColumns = false;
- }
+ colSel = hiddenColumns;
}
init();
}
- void init()
+ /**
+ * Apply any settings saved in user preferences
+ */
+ private void applyViewProperties()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
-
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
- showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
- showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+ viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
+ setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
- rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
- centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
+ setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+ setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
setPadGaps(Cache.getDefault("PAD_GAPS", true));
- shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
- showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
+ setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+ viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
+ viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
+ viewStyle.setShowUnconserved(Cache
+ .getDefault("SHOW_UNCONSERVED", false));
+ sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+ followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+ sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
+ Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
+ viewStyle.setScaleProteinAsCdna(Cache.getDefault(
+ Preferences.SCALE_PROTEIN_TO_CDNA, true));
+ }
+
+ void init()
+ {
+ this.startRes = 0;
+ this.endRes = alignment.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = alignment.getHeight() - 1;
+ applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
String fontSize = Cache.getDefault("FONT_SIZE", "10");
- seqNameItalics = Cache.getDefault("ID_ITALICS", true);
-
int style = 0;
if (fontStyle.equals("bold"))
style = 2;
}
- setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
alignment
.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
{
if (!alignment.isNucleotide())
{
- showConservation=Cache.getDefault("SHOW_CONSERVATION", true);
- showQuality=Cache.getDefault("SHOW_QUALITY", true);
+ showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+ showQuality = Cache.getDefault("SHOW_QUALITY", true);
showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
false);
- }
+ }
showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
- normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false);
+ normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+ false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
- showConsensus=Cache.getDefault("SHOW_IDENTITY", true);
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
+ showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
}
initAutoAnnotation();
- if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+ String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT;
+ String propertyValue = Cache.getProperty(colourProperty);
+ if (propertyValue == null)
+ {
+ // fall back on this property for backwards compatibility
+ propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+ }
+ if (propertyValue != null)
{
globalColourScheme = ColourSchemeProperty.getColour(alignment,
- jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+ propertyValue);
if (globalColourScheme instanceof UserColourScheme)
{
globalColourScheme = UserDefinedColours.loadDefaultColours();
((UserColourScheme) globalColourScheme).setThreshold(0,
- getIgnoreGapsConsensus());
+ isIgnoreGapsConsensus());
}
if (globalColourScheme != null)
globalColourScheme.setConsensus(hconsensus);
}
}
-
- wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
- false);
- sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
- followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
- true);
- }
-
- /**
- * set the flag
- *
- * @param b
- * features are displayed if true
- */
- public void setShowSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
- }
-
- public boolean getShowSequenceFeatures()
- {
- return showSequenceFeatures;
}
/**
- * centre columnar annotation labels in displayed alignment annotation TODO:
- * add to jalviewXML and annotation display settings
- */
- boolean centreColumnLabels = false;
-
- private boolean showdbrefs;
-
- private boolean shownpfeats;
-
- // --------END Structure Conservation
-
- /**
* get the consensus sequence as displayed under the PID consensus annotation
* row.
*
return sq;
}
+ boolean validCharWidth;
+
/**
- * DOCUMENT ME!
+ * update view settings with the given font. You may need to call
+ * alignPanel.fontChanged to update the layout geometry
*
- * @return DOCUMENT ME!
+ * @param setGrid
+ * when true, charWidth/height is set according to font mentrics
*/
- public int getStartRes()
+ public void setFont(Font f, boolean setGrid)
{
- return startRes;
+ font = f;
+
+ Container c = new Container();
+
+ java.awt.FontMetrics fm = c.getFontMetrics(font);
+ int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
+ .getCharHeight();
+ if (setGrid)
+ {
+ setCharHeight(fm.getHeight());
+ setCharWidth(ww);
+ }
+ viewStyle.setFontName(font.getName());
+ viewStyle.setFontStyle(font.getStyle());
+ viewStyle.setFontSize(font.getSize());
+
+ validCharWidth = true;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEndRes()
+ @Override
+ public void setViewStyle(ViewStyleI settingsForView)
{
- return endRes;
+ super.setViewStyle(settingsForView);
+ setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
+ viewStyle.getFontSize()), false);
+
}
/**
*
* @return DOCUMENT ME!
*/
- public int getStartSeq()
+ public Font getFont()
{
- return startSeq;
+ return font;
}
/**
* DOCUMENT ME!
*
- * @param res
+ * @param align
* DOCUMENT ME!
*/
- public void setStartRes(int res)
+ public void setAlignment(AlignmentI align)
{
- this.startRes = res;
+ replaceMappings(align);
+ this.alignment = align;
}
/**
- * DOCUMENT ME!
+ * Replace any codon mappings for this viewport with those for the given
+ * viewport
*
- * @param seq
- * DOCUMENT ME!
+ * @param align
*/
- public void setStartSeq(int seq)
+ public void replaceMappings(AlignmentI align)
{
- this.startSeq = seq;
- }
- /**
- * DOCUMENT ME!
- *
- * @param res
- * DOCUMENT ME!
- */
- public void setEndRes(int res)
- {
- if (res > (alignment.getWidth() - 1))
+ /*
+ * Deregister current mappings (if any)
+ */
+ deregisterMappings();
+
+ /*
+ * Register new mappings (if any)
+ */
+ if (align != null)
{
- // log.System.out.println(" Corrected res from " + res + " to maximum " +
- // (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerMappings(align.getCodonFrames());
}
- if (res < 0)
+ /*
+ * replace mappings on our alignment
+ */
+ if (alignment != null && align != null)
{
- res = 0;
+ alignment.setCodonFrames(align.getCodonFrames());
}
-
- this.endRes = res;
}
- /**
- * DOCUMENT ME!
- *
- * @param seq
- * DOCUMENT ME!
- */
- public void setEndSeq(int seq)
+ protected void deregisterMappings()
{
- if (seq > alignment.getHeight())
+ AlignmentI al = getAlignment();
+ if (al != null)
{
- seq = alignment.getHeight();
- }
-
- if (seq < 0)
- {
- seq = 0;
+ Set<AlignedCodonFrame> mappings = al.getCodonFrames();
+ if (mappings != null)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ for (AlignedCodonFrame acf : mappings)
+ {
+ if (noReferencesTo(acf))
+ {
+ ssm.deregisterMapping(acf);
+ }
+ }
+ }
}
-
- this.endSeq = seq;
}
/**
*
* @return DOCUMENT ME!
*/
- public int getEndSeq()
+ public char getGapCharacter()
{
- return endSeq;
+ return getAlignment().getGapCharacter();
}
/**
* DOCUMENT ME!
*
- * @param f
+ * @param gap
* DOCUMENT ME!
*/
- public void setFont(Font f)
+ public void setGapCharacter(char gap)
{
- font = f;
-
- Container c = new Container();
-
- java.awt.FontMetrics fm = c.getFontMetrics(font);
- setCharHeight(fm.getHeight());
- setCharWidth(fm.charWidth('M'));
- validCharWidth = true;
+ if (getAlignment() != null)
+ {
+ getAlignment().setGapCharacter(gap);
+ }
}
/**
*
* @return DOCUMENT ME!
*/
- public Font getFont()
+ public ColumnSelection getColumnSelection()
{
- return font;
+ return colSel;
}
/**
* DOCUMENT ME!
*
- * @param w
+ * @param tree
* DOCUMENT ME!
*/
- public void setCharWidth(int w)
+ public void setCurrentTree(NJTree tree)
{
- this.charWidth = w;
+ currentTree = tree;
}
/**
*
* @return DOCUMENT ME!
*/
- public int getCharWidth()
+ public NJTree getCurrentTree()
{
- return charWidth;
+ return currentTree;
}
/**
- * DOCUMENT ME!
+ * returns the visible column regions of the alignment
*
- * @param h
- * DOCUMENT ME!
+ * @param selectedRegionOnly
+ * true to just return the contigs intersecting with the selected
+ * area
+ * @return
*/
- public void setCharHeight(int h)
+ public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
{
- this.charHeight = h;
+ int[] viscontigs = null;
+ int start = 0, end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ viscontigs = colSel.getVisibleContigs(start, end);
+ return viscontigs;
}
/**
- * DOCUMENT ME!
+ * get hash of undo and redo list for the alignment
*
- * @return DOCUMENT ME!
+ * @return long[] { historyList.hashCode, redoList.hashCode };
*/
- public int getCharHeight()
+ public long[] getUndoRedoHash()
{
- return charHeight;
+ // TODO: JAL-1126
+ if (historyList == null || redoList == null)
+ {
+ return new long[] { -1, -1 };
+ }
+ return new long[] { historyList.hashCode(), this.redoList.hashCode() };
}
/**
- * DOCUMENT ME!
+ * test if a particular set of hashcodes are different to the hashcodes for
+ * the undo and redo list.
*
- * @param w
- * DOCUMENT ME!
+ * @param undoredo
+ * the stored set of hashcodes as returned by getUndoRedoHash
+ * @return true if the hashcodes differ (ie the alignment has been edited) or
+ * the stored hashcode array differs in size
*/
- public void setWrappedWidth(int w)
+ public boolean isUndoRedoHashModified(long[] undoredo)
{
- this.wrappedWidth = w;
+ if (undoredo == null)
+ {
+ return true;
+ }
+ long[] cstate = getUndoRedoHash();
+ if (cstate.length != undoredo.length)
+ {
+ return true;
+ }
+
+ for (int i = 0; i < cstate.length; i++)
+ {
+ if (cstate[i] != undoredo[i])
+ {
+ return true;
+ }
+ }
+ return false;
}
+ public boolean followSelection = true;
+
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
*/
- public int getWrappedWidth()
+ public boolean getFollowSelection()
{
- return wrappedWidth;
+ return followSelection;
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Send the current selection to be broadcast to any selection listeners.
*/
- public AlignmentI getAlignment()
+ public void sendSelection()
{
- return alignment;
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
}
/**
- * DOCUMENT ME!
+ * return the alignPanel containing the given viewport. Use this to get the
+ * components currently handling the given viewport.
*
- * @param align
- * DOCUMENT ME!
+ * @param av
+ * @return null or an alignPanel guaranteed to have non-null alignFrame
+ * reference
*/
- public void setAlignment(AlignmentI align)
+ public AlignmentPanel getAlignPanel()
{
- if (alignment != null && alignment.getCodonFrames() != null)
- {
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).removeMappings(alignment.getCodonFrames());
- }
- this.alignment = align;
- if (alignment!=null && alignment.getCodonFrames() != null)
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+ .getSequenceSetId());
+ for (int p = 0; aps != null && p < aps.length; p++)
{
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).addMappings(alignment.getCodonFrames());
+ if (aps[p].av == this)
+ {
+ return aps[p];
+ }
}
+ return null;
}
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setWrapAlignment(boolean state)
- {
- wrapAlignment = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowText(boolean state)
- {
- showText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setRenderGaps(boolean state)
- {
- renderGaps = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourText()
- {
- return showColourText;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setColourText(boolean state)
- {
- showColourText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowBoxes(boolean state)
- {
- showBoxes = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getWrapAlignment()
- {
- return wrapAlignment;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowText()
- {
- return showText;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowBoxes()
+ public boolean getSortByTree()
{
- return showBoxes;
+ return sortByTree;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getGapCharacter()
+ public void setSortByTree(boolean sort)
{
- return getAlignment().getGapCharacter();
+ sortByTree = sort;
}
/**
- * DOCUMENT ME!
+ * synthesize a column selection if none exists so it covers the given
+ * selection group. if wholewidth is false, no column selection is made if the
+ * selection group covers the whole alignment width.
*
- * @param gap
- * DOCUMENT ME!
+ * @param sg
+ * @param wholewidth
*/
- public void setGapCharacter(char gap)
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
{
- if (getAlignment() != null)
+ int sgs, sge;
+ if (sg != null
+ && (sgs = sg.getStartRes()) >= 0
+ && sg.getStartRes() <= (sge = sg.getEndRes())
+ && (colSel == null || colSel.getSelected() == null || colSel
+ .getSelected().size() == 0))
{
- getAlignment().setGapCharacter(gap);
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+ {
+ // do nothing
+ return;
+ }
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
+ }
}
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Returns the (Desktop) instance of the StructureSelectionManager
*/
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setCurrentTree(NJTree tree)
- {
- currentTree = tree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public NJTree getCurrentTree()
- {
- return currentTree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setShowJVSuffix(boolean b)
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
{
- showJVSuffix = b;
+ return StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
}
/**
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @param pdbEntries
+ * @return an array of SequenceI arrays, one for each PDBEntry, listing which
+ * sequences in the alignment hold a reference to it
*/
- public boolean getShowAnnotation()
+ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
{
- return showAnnotation;
+ List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ for (PDBEntry pdb : pdbEntries)
+ {
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ for (SequenceI sq : alignment.getSequences())
+ {
+ Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
+ if (pdbs == null)
+ {
+ continue;
+ }
+ for (PDBEntry p1 : pdbs)
+ {
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq))
+ {
+ seqs.add(sq);
+ continue;
+ }
+ }
+ }
+ }
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setShowAnnotation(boolean b)
+ public boolean isNormaliseSequenceLogo()
{
- showAnnotation = b;
+ return normaliseSequenceLogo;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleAboveWrapped()
+ public void setNormaliseSequenceLogo(boolean state)
{
- return scaleAboveWrapped;
+ normaliseSequenceLogo = state;
}
/**
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return true if alignment characters should be displayed
*/
- public boolean getScaleLeftWrapped()
+ public boolean isValidCharWidth()
{
- return scaleLeftWrapped;
+ return validCharWidth;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleAboveWrapped(boolean b)
+ public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
- scaleAboveWrapped = b;
+ return calcIdParams.get(calcId);
}
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleLeftWrapped(boolean b)
+ public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+ boolean needsUpdate)
{
- scaleLeftWrapped = b;
+ calcIdParams.put(calcId, settings);
+ // TODO: create a restart list to trigger any calculations that need to be
+ // restarted after load
+ // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
+ if (needsUpdate)
+ {
+ Cache.log.debug("trigger update for " + calcId);
+ }
}
/**
- * DOCUMENT ME!
+ * Method called when another alignment's edit (or possibly other) command is
+ * broadcast to here.
+ *
+ * To allow for sequence mappings (e.g. protein to cDNA), we have to first
+ * 'unwind' the command on the source sequences (in simulation, not in fact),
+ * and then for each edit in turn:
+ * <ul>
+ * <li>compute the equivalent edit on the mapped sequences</li>
+ * <li>apply the mapped edit</li>
+ * <li>'apply' the source edit to the working copy of the source sequences</li>
+ * </ul>
*
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
-
-
- public void setDataset(boolean b)
- {
- isDataset = b;
- }
-
- public boolean isDataset()
- {
- return isDataset;
- }
-
-
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
-
- public Color getSequenceColour(SequenceI seq)
- {
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
+ * @param command
+ * @param undo
+ * @param ssm
+ */
+ @Override
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source)
+ {
+ /*
+ * Do nothing unless we are a 'complement' of the source. May replace this
+ * with direct calls not via SSM.
+ */
+ if (source instanceof AlignViewportI
+ && ((AlignViewportI) source).getCodingComplement() == this)
{
- return Color.white;
+ // ok to continue;
}
else
{
- return (Color) sequenceColours.get(seq);
+ return;
}
- }
- public void setSequenceColour(SequenceI seq, Color col)
- {
- if (sequenceColours == null)
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+ getGapCharacter());
+ if (mappedCommand != null)
{
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
+ AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
+ mappedCommand.doCommand(views);
+ getAlignPanel().alignmentChanged();
}
}
/**
- * returns the visible column regions of the alignment
+ * Add the sequences from the given alignment to this viewport. Optionally,
+ * may give the user the option to open a new frame, or split panel, with cDNA
+ * and protein linked.
*
- * @param selectedRegionOnly
- * true to just return the contigs intersecting with the selected
- * area
- * @return
+ * @param al
+ * @param title
*/
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ public void addAlignment(AlignmentI al, String title)
{
- int[] viscontigs = null;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
+ // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
+
+ // JBPComment: title is a largely redundant parameter at the moment
+ // JBPComment: this really should be an 'insert/pre/append' controller
+ // JBPComment: but the DNA/Protein check makes it a bit more complex
+
+ // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
+ // this comment:
+ // TODO: create undo object for this JAL-1101
+
+ /*
+ * If any cDNA/protein mappings can be made between the alignments, offer to
+ * open a linked alignment with split frame option.
+ */
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes() + 1;
+ if (al.getDataset() == null)
+ {
+ // need to create ds seqs
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() == null)
+ {
+ sq.createDatasetSequence();
+ }
+ }
+ }
+ if (AlignmentUtils.isMappable(al, getAlignment()))
+ {
+ if (openLinkedAlignment(al, title))
+ {
+ return;
+ }
+ }
}
- else
+
+ /*
+ * No mappings, or offer declined - add sequences to this alignment
+ */
+ // TODO: JAL-407 regardless of above - identical sequences (based on ID and
+ // provenance) should share the same dataset sequence
+
+ for (int i = 0; i < al.getHeight(); i++)
{
- end = alignment.getWidth();
+ getAlignment().addSequence(al.getSequenceAt(i));
}
- viscontigs = colSel.getVisibleContigs(start, end);
- return viscontigs;
- }
- /**
- * get hash of undo and redo list for the alignment
- *
- * @return long[] { historyList.hashCode, redoList.hashCode };
- */
- public long[] getUndoRedoHash()
- {
- // TODO: JAL-1126
- if (historyList == null || redoList == null)
- return new long[]
- { -1, -1 };
- return new long[]
- { historyList.hashCode(), this.redoList.hashCode() };
+ setEndSeq(getAlignment().getHeight());
+ firePropertyChange("alignment", null, getAlignment().getSequences());
}
/**
- * test if a particular set of hashcodes are different to the hashcodes for
- * the undo and redo list.
+ * Show a dialog with the option to open and link (cDNA <-> protein) as a new
+ * alignment, either as a standalone alignment or in a split frame. Returns
+ * true if the new alignment was opened, false if not, because the user
+ * declined the offer.
*
- * @param undoredo
- * the stored set of hashcodes as returned by getUndoRedoHash
- * @return true if the hashcodes differ (ie the alignment has been edited) or
- * the stored hashcode array differs in size
- */
- public boolean isUndoRedoHashModified(long[] undoredo)
- {
- if (undoredo == null)
+ * @param al
+ * @param title
+ */
+ protected boolean openLinkedAlignment(AlignmentI al, String title)
+ {
+ String[] options = new String[] {
+ MessageManager.getString("action.no"),
+ MessageManager.getString("label.split_window"),
+ MessageManager.getString("label.new_window"), };
+ final String question = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.open_split_window?"));
+ int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ MessageManager.getString("label.open_split_window"),
+ JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+
+ if (response != 1 && response != 2)
{
- return true;
+ return false;
}
- long[] cstate = getUndoRedoHash();
- if (cstate.length != undoredo.length)
+ final boolean openSplitPane = (response == 1);
+ final boolean openInNewWindow = (response == 2);
+
+ /*
+ * Identify protein and dna alignments. Make a copy of this one if opening
+ * in a new split pane.
+ */
+ AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ : getAlignment();
+ AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+ /*
+ * Map sequences. At least one should get mapped as we have already passed
+ * the test for 'mappability'. Any mappings made will be added to the
+ * protein alignment. Note creating dataset sequences on the new alignment
+ * is a pre-requisite for building mappings.
+ */
+ al.setDataset(null);
+ AlignmentUtils.mapProteinToCdna(protein, cdna);
+
+ /*
+ * Create the AlignFrame for the added alignment. If it is protein, mappings
+ * are registered with StructureSelectionManager as a side-effect.
+ */
+ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ newAlignFrame.setTitle(title);
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new Object[] { title }));
+
+ // TODO if we want this (e.g. to enable reload of the alignment from file),
+ // we will need to add parameters to the stack.
+ // if (!protocol.equals(AppletFormatAdapter.PASTE))
+ // {
+ // alignFrame.setFileName(file, format);
+ // }
+
+ if (openInNewWindow)
{
- return true;
+ Desktop.addInternalFrame(newAlignFrame, title,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
- for (int i = 0; i < cstate.length; i++)
+ try
{
- if (cstate[i] != undoredo[i])
- {
- return true;
- }
- }
- return false;
- }
-
- public boolean getCentreColumnLabels()
- {
- return centreColumnLabels;
- }
-
- public void setCentreColumnLabels(boolean centrecolumnlabels)
- {
- centreColumnLabels = centrecolumnlabels;
- }
-
- public void updateSequenceIdColours()
- {
- if (sequenceColours == null)
+ newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
{
- sequenceColours = new Hashtable();
}
- for (SequenceGroup sg:alignment.getGroups())
+
+ if (openSplitPane)
{
- if (sg.idColour != null)
- {
- for (SequenceI s:sg.getSequences(getHiddenRepSequences()))
- {
- sequenceColours.put(s, sg.idColour);
- }
- }
+ al.alignAs(thisAlignment);
+ protein = openSplitFrame(newAlignFrame, thisAlignment);
}
- }
- /**
- * enable or disable the display of Database Cross References in the sequence
- * ID tooltip
- */
- public void setShowDbRefs(boolean show)
- {
- showdbrefs = show;
+ return true;
}
/**
+ * Helper method to open a new SplitFrame holding linked dna and protein
+ * alignments.
*
- * @return true if Database References are to be displayed on tooltips.
+ * @param newAlignFrame
+ * containing a new alignment to be shown
+ * @param complement
+ * cdna/protein complement alignment to show in the other split half
+ * @return the protein alignment in the split frame
*/
- public boolean isShowDbRefs()
+ protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
+ AlignmentI complement)
{
- return showdbrefs;
- }
+ /*
+ * Make a new frame with a copy of the alignment we are adding to. If this
+ * is protein, the mappings to cDNA will be registered with
+ * StructureSelectionManager as a side-effect.
+ */
+ AlignFrame copyMe = new AlignFrame(complement,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
- /**
- *
- * @return true if Non-positional features are to be displayed on tooltips.
- */
- public boolean isShowNpFeats()
- {
- return shownpfeats;
- }
+ AlignmentI al = newAlignFrame.viewport.getAlignment();
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
- /**
- * enable or disable the display of Non-Positional sequence features in the
- * sequence ID tooltip
- *
- * @param show
- */
- public void setShowNpFeats(boolean show)
- {
- shownpfeats = show;
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+
+ return proteinFrame.viewport.getAlignment();
}
- /**
- *
- * @return true if view has hidden rows
- */
- public boolean hasHiddenRows()
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
{
- return hasHiddenRows;
+ return annotationColumnSelectionState;
}
- /**
- *
- * @return true if view has hidden columns
- */
- public boolean hasHiddenColumns()
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser currentAnnotationColumnSelectionState)
{
- return hasHiddenColumns;
+ this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
}
- /**
- * when set, view will scroll to show the highlighted position
- */
- public boolean followHighlight = true;
-
- /**
- * @return true if view should scroll to show the highlighted region of a
- * sequence
- * @return
- */
- public boolean getFollowHighlight()
+ @Override
+ public void setIdWidth(int i)
{
- return followHighlight;
+ super.setIdWidth(i);
+ AlignmentPanel ap = getAlignPanel();
+ if (ap != null)
+ {
+ // modify GUI elements to reflect geometry change
+ Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
+ .getPreferredSize();
+ idw.width = i;
+ getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+ }
}
- public boolean followSelection = true;
-
- /**
- * @return true if view selection should always follow the selections
- * broadcast by other selection sources
- */
- public boolean getFollowSelection()
+ public Rectangle getExplodedGeometry()
{
- return followSelection;
+ return explodedGeometry;
}
- boolean showSeqFeaturesHeight;
-
- public void sendSelection()
+ public void setExplodedGeometry(Rectangle explodedPosition)
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
+ this.explodedGeometry = explodedPosition;
}
- public void setShowSequenceFeaturesHeight(boolean selected)
+ public boolean isGatherViewsHere()
{
- showSeqFeaturesHeight = selected;
+ return gatherViewsHere;
}
- public boolean getShowSequenceFeaturesHeight()
+ public void setGatherViewsHere(boolean gatherViewsHere)
{
- return showSeqFeaturesHeight;
+ this.gatherViewsHere = gatherViewsHere;
}
/**
- * return the alignPanel containing the given viewport. Use this to get the
- * components currently handling the given viewport.
- *
- * @param av
- * @return null or an alignPanel guaranteed to have non-null alignFrame
- * reference
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
*/
- public AlignmentPanel getAlignPanel()
+ public void scrollComplementaryAlignment()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
- .getSequenceSetId());
- AlignmentPanel ap = null;
- for (int p = 0; aps != null && p < aps.length; p++)
+ /*
+ * Populate a SearchResults object with the mapped location to scroll to. If
+ * there is no complement, or it is not following highlights, or no mapping
+ * is found, the result will be empty.
+ */
+ SearchResults sr = new SearchResults();
+ int verticalOffset = findComplementScrollTarget(sr);
+ if (!sr.isEmpty())
{
- if (aps[p].av == this)
- {
- return aps[p];
- }
+ // TODO would like next line without cast but needs more refactoring...
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+ .getAlignPanel();
+ complementPanel.setFollowingComplementScroll(true);
+ complementPanel.scrollToCentre(sr, verticalOffset);
}
- return null;
- }
-
- public boolean getSortByTree()
- {
- return sortByTree;
- }
-
- public void setSortByTree(boolean sort)
- {
- sortByTree = sort;
}
/**
- * synthesize a column selection if none exists so it covers the given
- * selection group. if wholewidth is false, no column selection is made if the
- * selection group covers the whole alignment width.
+ * Answers true if no alignment holds a reference to the given mapping
*
- * @param sg
- * @param wholewidth
+ * @param acf
+ * @return
*/
- public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+ protected boolean noReferencesTo(AlignedCodonFrame acf)
{
- int sgs, sge;
- if (sg != null
- && (sgs = sg.getStartRes()) >= 0
- && sg.getStartRes() <= (sge = sg.getEndRes())
- && (colSel == null || colSel.getSelected() == null || colSel
- .getSelected().size() == 0))
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames == null)
{
- if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
- {
- // do nothing
- return;
- }
- if (colSel == null)
- {
- colSel = new ColumnSelection();
- }
- for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
- {
- colSel.addElement(cspos);
- }
+ return true;
}
- }
-
- public StructureSelectionManager getStructureSelectionManager()
- {
- return StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- }
-
- /**
- *
- * @param pdbEntries
- * @return a series of SequenceI arrays, one for each PDBEntry, listing which
- * sequence in the alignment holds a reference to it
- */
- public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
- {
- ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
- for (PDBEntry pdb : pdbEntries)
+ for (AlignFrame af : frames)
{
- ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
- for (int i = 0; i < alignment.getHeight(); i++)
+ if (!af.isClosed())
{
- Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
- .getPDBId();
- if (pdbs == null)
- continue;
- SequenceI sq;
- for (int p = 0; p < pdbs.size(); p++)
+ for (AlignmentViewPanel ap : af.getAlignPanels())
{
- PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
- if (p1.getId().equals(pdb.getId()))
+ AlignmentI al = ap.getAlignment();
+ if (al != null && al.getCodonFrames().contains(acf))
{
- if (!seqs.contains(sq = alignment.getSequenceAt(i)))
- seqs.add(sq);
-
- continue;
+ return false;
}
}
}
- seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
}
- return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
- }
-
-
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
+ return true;
}
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
-
- /**
- *
- * @return true if alignment characters should be displayed
- */
- public boolean isValidCharWidth()
- {
- return validCharWidth;
- }
- private Hashtable<String, AutoCalcSetting> calcIdParams=new Hashtable<String, AutoCalcSetting>();
- public AutoCalcSetting getCalcIdSettingsFor(String calcId)
- {
- return calcIdParams.get(calcId);
- }
-
- public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings, boolean needsUpdate)
- {
- calcIdParams.put(calcId, settings);
- // TODO: create a restart list to trigger any calculations that need to be restarted after load
- // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
- }
-
}
git://source.jalview.org / jalview.git / blobdiff